OpenRaiser/Intern-Atlas huggingface dataset:
Automating Data-Driven Modeling and Analysis for Engineering Applications using Large Language Model Agents
Venue: arXiv cs.AI 2025
Year: 2025

Modern engineering increasingly relies on vast datasets generated by experiments and simulations, driving a growing demand for efficient, reliable, and broadly applicable modeling strategies. There is also heightened interest in developing data-driven approaches, particularly neural network models, for effective prediction and analysis of scientific datasets. Traditional data-driven methods frequently involve extensive manual intervention, limiting their ability to scale effectively and generalize to diverse applications. In this study, we propose an innovative pipeline utilizing Large Language Model (LLM) agents to automate data-driven modeling and analysis, with a particular emphasis on regression tasks. We evaluate two LLM-agent frameworks: a multi-agent system featuring specialized collaborative agents, and a single-agent system based on the Reasoning and Acting (ReAct) paradigm. Both frameworks autonomously handle data preprocessing, neural network development, training, hyperparameter optimization, and uncertainty quantification (UQ). We validate our approach using a critical heat flux (CHF) prediction benchmark, involving approximately 25,000 experimental data points from the OECD/NEA benchmark dataset. Results indicate that our LLM-agent-developed model surpasses traditional CHF lookup tables and delivers predictive accuracy and UQ on par with state-of-the-art Bayesian optimized deep neural network models developed by human experts. These outcomes underscore the significant potential of LLM-based agents to automate complex engineering modeling tasks, greatly reducing human workload while meeting or exceeding existing standards of predictive performance.
OntoLogX: Ontology-Guided Knowledge Graph Extraction from Cybersecurity Logs with Large Language Models
Venue: arXiv cs.AI 2025
Year: 2025

System logs represent a valuable source of Cyber Threat Intelligence (CTI), capturing attacker behaviors, exploited vulnerabilities, and traces of malicious activity. Yet their utility is often limited by lack of structure, semantic inconsistency, and fragmentation across devices and sessions. Extracting actionable CTI from logs therefore requires approaches that can reconcile noisy, heterogeneous data into coherent and interoperable representations. We introduce OntoLogX, an autonomous Artificial Intelligence (AI) agent that leverages Large Language Models (LLMs) to transform raw logs into ontology-grounded Knowledge Graphs (KGs). OntoLogX integrates a lightweight log ontology with Retrieval Augmented Generation (RAG) and iterative correction steps, ensuring that generated KGs are syntactically and semantically valid. Beyond event-level analysis, the system aggregates KGs into sessions and employs a LLM to predict MITRE ATT&CK tactics, linking low-level log evidence to higher-level adversarial objectives. We evaluate OntoLogX on both logs from a public benchmark and a real-world honeypot dataset, demonstrating robust KG generation across multiple KGs backends and accurate mapping of adversarial activity to ATT&CK tactics. Results highlight the benefits of retrieval and correction for precision and recall, the effectiveness of code-oriented models in structured log analysis, and the value of ontology-grounded representations for actionable CTI extraction.
On the Role of Domain Experts in Creating Effective Tutoring Systems
Venue: arXiv cs.AI 2025
Year: 2025

The role that highly curated knowledge, provided by domain experts, could play in creating effective tutoring systems is often overlooked within the AI for education community. In this paper, we highlight this topic by discussing two ways such highly curated expert knowledge could help in creating novel educational systems. First, we will look at how one could use explainable AI (XAI) techniques to automatically create lessons. Most existing XAI methods are primarily aimed at debugging AI systems. However, we will discuss how one could use expert specified rules about solving specific problems along with novel XAI techniques to automatically generate lessons that could be provided to learners. Secondly, we will see how an expert specified curriculum for learning a target concept can help develop adaptive tutoring systems, that can not only provide a better learning experience, but could also allow us to use more efficient algorithms to create these systems. Finally, we will highlight the importance of such methods using a case study of creating a tutoring system for pollinator identification, where such knowledge could easily be elicited from experts.
AFFORD2ACT: Affordance-Guided Automatic Keypoint Selection for Generalizable and Lightweight Robotic Manipulation
Venue: arXiv cs.RO 2025
Year: 2025

Vision-based robot learning often relies on dense image or point-cloud inputs, which are computationally heavy and entangle irrelevant background features. Existing keypoint-based approaches can focus on manipulation-centric features and be lightweight, but either depend on manual heuristics or task-coupled selection, limiting scalability and semantic understanding. To address this, we propose AFFORD2ACT, an affordance-guided framework that distills a minimal set of semantic 2D keypoints from a text prompt and a single image. AFFORD2ACT follows a three-stage pipeline: affordance filtering, category-level keypoint construction, and transformer-based policy learning with embedded gating to reason about the most relevant keypoints, yielding a compact 38-dimensional state policy that can be trained in 15 minutes, which performs well in real-time without proprioception or dense representations. Across diverse real-world manipulation tasks, AFFORD2ACT consistently improves data efficiency, achieving an 82% success rate on unseen objects, novel categories, backgrounds, and distractors.
Differentiable Skill Optimisation for Powder Manipulation in Laboratory Automation
Venue: arXiv cs.RO 2025
Year: 2025

Robotic automation is accelerating scientific discovery by reducing manual effort in laboratory workflows. However, precise manipulation of powders remains challenging, particularly in tasks such as transport that demand accuracy and stability. We propose a trajectory optimisation framework for powder transport in laboratory settings, which integrates differentiable physics simulation for accurate modelling of granular dynamics, low-dimensional skill-space parameterisation to reduce optimisation complexity, and a curriculum-based strategy that progressively refines task competence over long horizons. This formulation enables end-to-end optimisation of contact-rich robot trajectories while maintaining stability and convergence efficiency. Experimental results demonstrate that the proposed method achieves superior task success rates and stability compared to the reinforcement learning baseline.
SCOPED: Score-Curvature Out-of-distribution Proximity Evaluator for Diffusion
Venue: arXiv cs.LG 2025
Year: 2025

Out-of-distribution (OOD) detection is essential for reliable deployment of machine learning systems in vision, robotics, reinforcement learning, and beyond. We introduce Score-Curvature Out-of-distribution Proximity Evaluator for Diffusion (SCOPED), a fast and general-purpose OOD detection method for diffusion models that reduces the number of forward passes on the trained model by an order of magnitude compared to prior methods, outperforming most diffusion-based baselines and closely approaching the accuracy of the strongest ones. SCOPED is computed from a single diffusion model trained once on a diverse dataset, and combines the Jacobian trace and squared norm of the model's score function into a single test statistic. Rather than thresholding on a fixed value, we estimate the in-distribution density of SCOPED scores using kernel density estimation, enabling a flexible, unsupervised test that, in the simplest case, only requires a single forward pass and one Jacobian-vector product (JVP), made efficient by Hutchinson's trace estimator. On four vision benchmarks, SCOPED achieves competitive or state-of-the-art precision-recall scores despite its low computational cost. The same method generalizes to robotic control tasks with shared state and action spaces, identifying distribution shifts across reward functions and training regimes. These results position SCOPED as a practical foundation for fast and reliable OOD detection in real-world domains, including perceptual artifacts in vision, outlier detection in autoregressive models, exploration in reinforcement learning, and dataset curation for unsupervised training.
Extracting O*NET Features from the NLx Corpus to Build Public Use Aggregate Labor Market Data
Venue: arXiv cs.CY 2025
Year: 2025

Data from online job postings are difficult to access and are not built in a standard or transparent manner. Data included in the standard taxonomy and occupational information database (O*NET) are updated infrequently and based on small survey samples. We adopt O*NET as a framework for building natural language processing tools that extract structured information from job postings. We publish the Job Ad Analysis Toolkit (JAAT), a collection of open-source tools built for this purpose, and demonstrate its reliability and accuracy in out-of-sample and LLM-as-a-Judge testing. We extract more than 10 billion data points from more than 155 million online job ads provided by the National Labor Exchange (NLx) Research Hub, including O*NET tasks, occupation codes, tools, and technologies, as well as wages, skills, industry, and more features. We describe the construction of a dataset of occupation, state, and industry level features aggregated by monthly active jobs from 2015 - 2025. We illustrate the potential for research and future uses in education and workforce development.
MightyPPL: Verification of MITL with Past and Pnueli Modalities
Venue: arXiv cs.FL 2025
Year: 2025

Metric Interval Temporal Logic (MITL) is a popular formalism for specifying properties of reactive systems with timing constraints. Existing approaches to using MITL in verification tasks, however, have notable drawbacks: they either support only limited fragments of the logic or allow for only incomplete verification. This paper introduces MightyPPL, a new tool for translating formulae in Metric Interval Temporal Logic with Past and Pnueli modalities (MITPPL) over the pointwise semantics into timed automata. MightyPPL enables satisfiability and model checking of a much more expressive specification logic over both finite and infinite words and incorporates a number of performance optimisations, including a novel symbolic encoding of transitions and a symmetry reduction technique that leads to an exponential improvement in the number of reachable discrete states. For a given MITPPL formula, MightyPPL can generate either a network of timed automata or a single timed automaton that is language-equivalent and compatible with multiple verification back-ends, including Uppaal, TChecker, and LTSmin, which supports multi-core model checking. We evaluate the performance of the toolchain across various case studies and configuration options.
Predictive Modeling and Explainable AI for Veterinary Safety Profiles, Residue Assessment, and Health Outcomes Using Real-World Data and Physicochemical Properties
Venue: arXiv cs.LG 2025
Year: 2025

The safe use of pharmaceuticals in food-producing animals is vital to protect animal welfare and human food safety. Adverse events (AEs) may signal unexpected pharmacokinetic or toxicokinetic effects, increasing the risk of violative residues in the food chain. This study introduces a predictive framework for classifying outcomes (Death vs. Recovery) using ~1.28 million reports (1987-2025 Q1) from the U.S. FDA's OpenFDA Center for Veterinary Medicine. A preprocessing pipeline merged relational tables and standardized AEs through VeDDRA ontologies. Data were normalized, missing values imputed, and high-cardinality features reduced; physicochemical drug properties were integrated to capture chemical-residue links. We evaluated supervised models, including Random Forest, CatBoost, XGBoost, ExcelFormer, and large language models (Gemma 3-27B, Phi 3-12B). Class imbalance was addressed, such as undersampling and oversampling, with a focus on prioritizing recall for fatal outcomes. Ensemble methods(Voting, Stacking) and CatBoost performed best, achieving precision, recall, and F1-scores of 0.95. Incorporating Average Uncertainty Margin (AUM)-based pseudo-labeling of uncertain cases improved minority-class detection, particularly in ExcelFormer and XGBoost. Interpretability via SHAP identified biologically plausible predictors, including lung, heart, and bronchial disorders, animal demographics, and drug physicochemical properties. These features were strongly linked to fatal outcomes. Overall, the framework shows that combining rigorous data engineering, advanced machine learning, and explainable AI enables accurate, interpretable predictions of veterinary safety outcomes. The approach supports FARAD's mission by enabling early detection of high-risk drug-event profiles, strengthening residue risk assessment, and informing regulatory and clinical decision-making.
MetaSynth: Multi-Agent Metadata Generation from Implicit Feedback in Black-Box Systems
Venue: arXiv cs.IR 2025
Year: 2025

Meta titles and descriptions strongly shape engagement in search and recommendation platforms, yet optimizing them remains challenging. Search engine ranking models are black box environments, explicit labels are unavailable, and feedback such as click-through rate (CTR) arrives only post-deployment. Existing template, LLM, and retrieval-augmented approaches either lack diversity, hallucinate attributes, or ignore whether candidate phrasing has historically succeeded in ranking. This leaves a gap in directly leveraging implicit signals from observable outcomes. We introduce MetaSynth, a multi-agent retrieval-augmented generation framework that learns from implicit search feedback. MetaSynth builds an exemplar library from top-ranked results, generates candidate snippets conditioned on both product content and exemplars, and iteratively refines outputs via evaluator-generator loops that enforce relevance, promotional strength, and compliance. On both proprietary e-commerce data and the Amazon Reviews corpus, MetaSynth outperforms strong baselines across NDCG, MRR, and rank metrics. Large-scale A/B tests further demonstrate 10.26% CTR and 7.51% clicks. Beyond metadata, this work contributes a general paradigm for optimizing content in black-box systems using implicit signals.
Growing Visual Generative Capacity for Pre-Trained MLLMs
Venue: arXiv cs.CV 2025
Year: 2025

Multimodal large language models (MLLMs) extend the success of language models to visual understanding, and recent efforts have sought to build unified MLLMs that support both understanding and generation. However, constructing such models remains challenging: hybrid approaches combine continuous embeddings with diffusion or flow-based objectives, producing high-quality images but breaking the autoregressive paradigm, while pure autoregressive approaches unify text and image prediction over discrete visual tokens but often face trade-offs between semantic alignment and pixel-level fidelity. In this work, we present Bridge, a pure autoregressive unified MLLM that augments pre-trained visual understanding models with generative ability through a Mixture-of-Transformers architecture, enabling both image understanding and generation within a single next-token prediction framework. To further improve visual generation fidelity, we propose a semantic-to-pixel discrete representation that integrates compact semantic tokens with fine-grained pixel tokens, achieving strong language alignment and precise description of visual details with only a 7.9% increase in sequence length. Extensive experiments across diverse multimodal benchmarks demonstrate that Bridge achieves competitive or superior results in both understanding and generation benchmarks, while requiring less training data and reduced training time compared to prior unified MLLMs.
Large-Scale Bayesian Causal Discovery with Interventional Data
Venue: arXiv cs.LG 2025
Year: 2025

Inferring the causal relationships among a set of variables in the form of a directed acyclic graph (DAG) is an important but notoriously challenging problem. Recently, advancements in high-throughput genomic perturbation screens have inspired development of methods that leverage interventional data to improve model identification. However, existing methods still suffer poor performance on large-scale tasks and fail to quantify uncertainty. Here, we propose Interventional Bayesian Causal Discovery (IBCD), an empirical Bayesian framework for causal discovery with interventional data. Our approach models the likelihood of the matrix of total causal effects, which can be approximated by a matrix normal distribution, rather than the full data matrix. We place a spike-and-slab horseshoe prior on the edges and separately learn data-driven weights for scale-free and Erdős-Rényi structures from observational data, treating each edge as a latent variable to enable uncertainty-aware inference. Through extensive simulation, we show that IBCD achieves superior structure recovery compared to existing baselines. We apply IBCD to CRISPR perturbation (Perturb-seq) data on 521 genes, demonstrating that edge posterior inclusion probabilities enable identification of robust graph structures.
A Novel Algorithm for Representing Positive Semi-Definite Polynomials as Sums of Squares with Rational Coefficients
Venue: arXiv cs.SC 2025
Year: 2025

This paper presents a novel algorithm for constructing a sum-of-squares (SOS) decomposition for positive semi-definite polynomials with rational coefficients. Unlike previous methods that typically yield SOS decompositions with floating-point coefficients, our approach ensures that all coefficients in the decomposition remain rational. This is particularly useful in formal verification and symbolic computation, where exact arithmetic is required. We introduce a stepwise reduction technique that transforms a given polynomial into a sum of ladder-like squares while preserving rationality. Experimental results demonstrate the effectiveness of our method compared to existing numerical approaches. This artical is an extension of the following Chinnese paper: HUANG Yong , ZENG Zhenbing , YANG Lu , RAO Yongsheng. An Algorithm to Represent Positive Semi-Definite Polynomials to Sum of Lader-Like Squares of Polynomials with Rational Coefficients (in Chinese). Journal of Systems Science and Mathematical Sciences, 2024, 44(5): 1241-1271 https://doi.org/10.12341/jssms23584CM
Guiding Multimodal Large Language Models with Blind and Low Vision People Visual Questions for Proactive Visual Interpretations
Venue: arXiv cs.CV 2025
Year: 2025

Multimodal large language models (MLLMs) have been integrated into visual interpretation applications to support Blind and Low Vision (BLV) users because of their accuracy and ability to provide rich, human-like interpretations. However, these applications often default to comprehensive, lengthy descriptions regardless of context. This leads to inefficient exchanges, as users must go through irrelevant details rather than receiving the specific information they are likely to seek. To deliver more contextually-relevant information, we developed a system that draws on historical BLV users questions. When given an image, our system identifies similar past visual contexts from the VizWiz-LF dataset and uses the associated questions to guide the MLLM generate descriptions more relevant to BLV users. An evaluation with three human labelers who revised 92 context-aware and context-free descriptions showed that context-aware descriptions anticipated and answered users' questions in 76.1% of cases (70 out of 92) and were preferred in 54.4% of comparisons (50 out of 92). Our paper reviews, and data analysis are publicly available in a Github repository at https://github.com/rgonzalezp/guiding-multimodal-large-language-models-with-blind-and-low-vision-people-visual-questions .
ReSSFormer: A Recursive Sparse Structured Transformer for Scalable and Long-Context Reasoning
Venue: arXiv cs.CL 2025
Year: 2025

While Transformer architectures have demonstrated impressive scalability across domains, they continue to face challenges in long-context reasoning, computational efficiency, and structural generalization - largely due to rigid layer stacking, dense attention, and reliance on positional encodings. We present ReSSFormer, a Recursive Sparse Structured Transformer that integrates three complementary innovations: Recurrent Reasoning & Memory Unit (R2MU) for iterative reasoning with bounded depth, Adaptive Sparse Attention Module (ASAM) for efficient and focused context selection, and Self-Organizing Encoder Structure (SOES) for position-free structure induction. ReSSFormer replaces conventional depth stacking with recurrent inference, substitutes full attention with token- and expert-level sparsity, and models latent token topology directly from content. Across language modeling, multi-hop QA, and structure-sensitive tasks, ReSSFormer consistently outperforms strong baselines under comparable FLOPs and parameter budgets, highlighting its scalability, efficiency, and structural flexibility.
AdvEvo-MARL: Shaping Internalized Safety through Adversarial Co-Evolution in Multi-Agent Reinforcement Learning
Venue: arXiv cs.AI 2025
Year: 2025

LLM-based multi-agent systems excel at planning, tool use, and role coordination, but their openness and interaction complexity also expose them to jailbreak, prompt-injection, and adversarial collaboration. Existing defenses fall into two lines: (i) self-verification that asks each agent to pre-filter unsafe instructions before execution, and (ii) external guard modules that police behaviors. The former often underperforms because a standalone agent lacks sufficient capacity to detect cross-agent unsafe chains and delegation-induced risks; the latter increases system overhead and creates a single-point-of-failure-once compromised, system-wide safety collapses, and adding more guards worsens cost and complexity. To solve these challenges, we propose AdvEvo-MARL, a co-evolutionary multi-agent reinforcement learning framework that internalizes safety into task agents. Rather than relying on external guards, AdvEvo-MARL jointly optimizes attackers (which synthesize evolving jailbreak prompts) and defenders (task agents trained to both accomplish their duties and resist attacks) in adversarial learning environments. To stabilize learning and foster cooperation, we introduce a public baseline for advantage estimation: agents within the same functional group share a group-level mean-return baseline, enabling lower-variance updates and stronger intra-group coordination. Across representative attack scenarios, AdvEvo-MARL consistently keeps attack-success rate (ASR) below 20%, whereas baselines reach up to 38.33%, while preserving-and sometimes improving-task accuracy (up to +3.67% on reasoning tasks). These results show that safety and utility can be jointly improved without relying on extra guard agents or added system overhead.